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Tue Jan 31 15:31:29 2023

Alex M

ARA Bicone Responses

Here we will record where we obtained the ARA bicone antenna response files we use as our baselines. We want to record where we found them/who gave them to us and how they were generated (either through simulation or from actual tests).

Tue Jul 2 13:16:30 2019

Julie Rolla

APS slides

The following are links to the 2018 and 2018 APS slides.

2018 APS talk:

https://www.dropbox.com/home/GP_Antennas/APS%20Talk?preview=April+APS+Talk_final.pdf

2019 APS talk:

https://absuploads.aps.org/presentation.cfm?pid=15183

202

Mon Mar 20 12:37:38 2023

Amy

ANITA/PUEO pictures

Here are some ANITA/PUEO pictures that I received from Christian Mike that might be helpful. I include his descriptions as well.

The one with the black crates in the background is the ANITA 1 and ANITA 2 form factor and the one in the anechoic chamber is the ANITA 3 and ANITA 4 form factor. I dimensioned out an ANITA 3/4 antenna, in CAD space, to give you a better idea of the ridge profile. The ANITA 1/2 CAD models we have, I found, are inaccurate.

Attached are images of the PUEO antenna array geometry. One image annotates the approximate locations of the Vpol feed with the top antenna feed as the origin.

Attachment 1: IMG_2362.jpg

Attachment 2: IMG_2364.jpg

Attachment 3: IMG_2365.jpg

Draft

Thu Jul 2 23:13:05 2020

Amy

A useful reference on bicone antennas

I found this datasheet on bicone antennas, that is a useful reference for seeing the relationship between bicone dimensions and bandwidth. From these it looks like the lower end of the band is at about f_low=c/(4*L_E), where L_E is the entire length of the antenna (twice the length of one cone), although we'd expect the peak gain to be where a quarter wavelength is just one of the cones (and the figure may roughly support that).

The attached file comes from this website:

https://www.ramayes.com/Biconical_Antennas.htm

Attachment 1: biconall.pdf

Tue Mar 5 16:36:51 2019

Julie Rolla

3/5 Task Updates

Tue Mar 5 17:29:02 2019

The things we worked on this week is in bold. Below the bold items is a description of exactly what we took care of.

Paper:
- Julie added Amy's edits.
- Julie let Kai know he is welcome to edit, too.
- Julie will also keep edits updated as they come in!
Get loop working-- specifically XF:
- Cade has now officially gotten reasonable outputs for his XF scripts. See the attached images for the XF outputs and associated CAD drawing. It seems to look like a reasonable gain pattern.
- The loop now works until AraSim. We are now getting the following AraSim errors:
  - XF_Loop.sh: line 244: ./AraSim: No such file or directory
  - XF_Loop.sh: line 244: ./AraSim: No such file or directory
- Julie is going to help Cade make sure that this directory is correct and that it has been compiled! More info to come.
Test GA (Suren):
- I've been working on creating a gaussian fitness score with which I can test the performance of our genetic algorithm. The idea is as follows: We run the GA and get a generation of individuals. We provide their fitness score by simply taking the values {radius, length, angle} as the {x, y, z} coordinate in a 3D space. We can then use a 3D gaussian to output a value at that location, and use that number as our fitness score. The beauty of this method is that we can then plot the progress of our genetic algorithm each generation as a dot in this 3D space, and we can see it slowly snake to the center. Additionally, we can use more complex fitness scores, like one with a local maxima and a global maxima to see if it get's stuck in the local maxima. Below, I have an image I generated on python of a 2D section contour plot of a 3D gaussian in length-angle space. The dark purple is a lower value and the yellow is a higher value of the gaussian. The lines and dots hand-drawn on top are an idea of what it would look for like to start the GA at the red dot and see it's progress each generation until it reaches the center, shown by the white dots. Running this for our current roulette algorithm would make a very nice GA proof of concept plot for the paper, I believe!
Gain pattern plots -- Make them 3D (Evelyn) & put on GitHub
- We need to figure out how to make a group Github. We have a lot of Githubs made by people and we need them all accessible from a group account. Right now the old dipole Github and the CalPoly stuff are linked to a group account. We need to find out how to get the Bicone account held by Max, and Evelyn's plotting code all on the group account: https://github.com/gp-antennas.
- Update: Evelyn and Max have contacted Brian to get their accounts linked. It looks like Amy, Brian, and Stephanie (Cal Poly) are the owners.
Insert LR plot & Gain plot to loop (?)
1. Edit bash script
2. Update Github
AraSim plots (Julie and Max) -- see #2 and #3 here: http://radiorm.physics.ohio-state.edu/elog/GENETIS/7 for details.
- Max and Julie have gotten sample data on Owens.
  - located at /users/PCON0003/cond0068/ARA/AraSim/branches/AraSimLite/outputs
- Max and Julie have gotten sample programs from Jorge.
  - https://github.com/toej93/AraSim_noise_calib/blob/master/readTree.cc
  - https://github.com/toej93/AraSim_noise_calib/blob/master/M.readTree
- Julie installed root, and had Max source Julie's thisroot.sh files to run root on Owens.
- Max installed Arasim to his user.
- Next step: run plotting software given by Jorge.
Update manual with things from Suren's last post here: http://radiorm.physics.ohio-state.edu/elog/GENETIS/8

Attachment 4: data.csv

Frequency (GHz),Theta (°),Phi (°),Gain phi,Gain theta
0.08333,0,0,4.19491965e-34,9.30908802e-36
0.08333,0,15.0000004,1.13745804e-34,2.83160959e-36
0.08333,0,30.0000008,2.90124587e-34,1.98981462e-34
0.08333,0,45.0000013,4.33400635e-34,3.34216749e-35
0.08333,0,60.0000017,2.87577966e-34,3.75231251e-34
0.08333,0,74.9999987,9.63247596e-35,1.39309362e-34
0.08333,0,90.0000025,2.77504471e-37,2.0774204e-34
0.08333,0,105,8.43720541e-35,1.15045184e-34
0.08333,0,120.000003,2.91249572e-34,3.04555617e-34
0.08333,0,135,2.34227902e-34,4.30943346e-34
0.08333,0,149.999997,1.06040209e-34,4.11289678e-34
0.08333,0,164.999994,7.50737618e-35,5.81275966e-36
0.08333,0,180.000005,1.78965268e-33,7.3492858e-37
0.08333,0,195.000002,2.02610741e-33,2.48287308e-35
0.08333,0,209.999999,8.89165876e-34,2.33583341e-35
0.08333,0,224.999996,3.16031794e-34,5.36348869e-34
0.08333,0,240.000007,1.47586622e-33,3.91377831e-35
0.08333,0,255.000004,2.87337932e-36,6.29063644e-34
0.08333,0,270.000001,1.31261981e-36,6.31632558e-34
0.08333,0,284.999998,1.8150178e-34,1.62607603e-34
0.08333,0,299.999995,5.04654556e-34,1.25443146e-33
0.08333,0,314.999992,1.93889207e-34,1.35787597e-34
0.08333,0,329.999989,2.98205296e-35,4.5730018e-34
0.08333,0,345.000013,2.06764199e-34,3.06302518e-35
0.08333,0,360.00001,4.19491965e-34,9.30908802e-36
0.08333,15.0000004,0,2.21307282e-12,0.0883042589
0.08333,15.0000004,15.0000004,1.24958681e-12,0.0883042738
0.08333,15.0000004,30.0000008,4.24763008e-13,0.0883042812
0.08333,15.0000004,45.0000013,1.43870359e-14,0.0883042961
0.08333,15.0000004,60.0000017,1.76734427e-13,0.0883042812
0.08333,15.0000004,74.9999987,8.30293787e-13,0.0883042738
0.08333,15.0000004,90.0000025,1.74207111e-12,0.0883042589
0.08333,15.0000004,105,2.68639538e-12,0.0883042738
0.08333,15.0000004,120.000003,3.48234115e-12,0.0883042812
0.08333,15.0000004,135,3.94334608e-12,0.0883042961
0.08333,15.0000004,149.999997,3.88229336e-12,0.0883042812
0.08333,15.0000004,164.999994,3.2406417e-12,0.0883042738
0.08333,15.0000004,180.000005,2.21092025e-12,0.0883042589
0.08333,15.0000004,195.000002,1.15119351e-12,0.0883042738
0.08333,15.0000004,209.999999,3.67093942e-13,0.0883042812
0.08333,15.0000004,224.999996,1.35828941e-14,0.0883042961
0.08333,15.0000004,240.000007,1.44884037e-13,0.0883042812
0.08333,15.0000004,255.000004,7.57448195e-13,0.0883042738
0.08333,15.0000004,270.000001,1.743383e-12,0.0883042589
0.08333,15.0000004,284.999998,2.82562493e-12,0.0883042738
0.08333,15.0000004,299.999995,3.63690545e-12,0.0883042812
0.08333,15.0000004,314.999992,3.93473708e-12,0.0883042961
0.08333,15.0000004,329.999989,3.70870695e-12,0.0883042812
0.08333,15.0000004,345.000013,3.08593168e-12,0.0883042738
0.08333,15.0000004,360.00001,2.21307282e-12,0.0883042589
0.08333,30.0000008,0,3.04286353e-11,0.330554247
0.08333,30.0000008,15.0000004,1.77038245e-11,0.330554426
0.08333,30.0000008,30.0000008,6.15558559e-12,0.330554664
0.08333,30.0000008,45.0000013,1.95957738e-13,0.330554813
0.08333,30.0000008,60.0000017,2.64734307e-12,0.330554664
0.08333,30.0000008,74.9999987,1.186425e-11,0.330554426
0.08333,30.0000008,90.0000025,2.39625351e-11,0.330554247
0.08333,30.0000008,105,3.62047961e-11,0.330554426
0.08333,30.0000008,120.000003,4.70035712e-11,0.330554664
0.08333,30.0000008,135,5.41321606e-11,0.330554813
0.08333,30.0000008,149.999997,5.42172245e-11,0.330554664
0.08333,30.0000008,164.999994,4.53593517e-11,0.330554426
0.08333,30.0000008,180.000005,3.04133004e-11,0.330554247
0.08333,30.0000008,195.000002,1.54130996e-11,0.330554426
0.08333,30.0000008,209.999999,4.83360053e-12,0.330554664
0.08333,30.0000008,224.999996,1.90661912e-13,0.330554813
0.08333,30.0000008,240.000007,1.83763486e-12,0.330554664
0.08333,30.0000008,255.000004,1.00491724e-11,0.330554426
0.08333,30.0000008,270.000001,2.39718714e-11,0.330554247
0.08333,30.0000008,284.999998,3.96109014e-11,0.330554426
0.08333,30.0000008,299.999995,5.08507958e-11,0.330554664
0.08333,30.0000008,314.999992,5.40794388e-11,0.330554813
0.08333,30.0000008,329.999989,5.01597201e-11,0.330554664
0.08333,30.0000008,345.000013,4.16781852e-11,0.330554426
0.08333,30.0000008,360.00001,3.04286353e-11,0.330554247
0.08333,45.0000013,0,1.19610113e-10,0.663833082
0.08333,45.0000013,15.0000004,7.04909117e-11,0.663833678
0.08333,45.0000013,30.0000008,2.47605096e-11,0.663835049
0.08333,45.0000013,45.0000013,7.7185464e-13,0.663835585
0.08333,45.0000013,60.0000017,1.07718721e-11,0.663835049
0.08333,45.0000013,74.9999987,4.7389391e-11,0.663833797
0.08333,45.0000013,90.0000025,9.42051992e-11,0.663833082
0.08333,45.0000013,105,1.41075526e-10,0.663833797
0.08333,45.0000013,120.000003,1.83183593e-10,0.663835049
0.08333,45.0000013,135,2.12397419e-10,0.663835585
0.08333,45.0000013,149.999997,2.1427396e-10,0.663835049
0.08333,45.0000013,164.999994,1.79498763e-10,0.663833678
0.08333,45.0000013,180.000005,1.19567467e-10,0.663833082
0.08333,45.0000013,195.000002,5.99928648e-11,0.663833678
0.08333,45.0000013,209.999999,1.8719401e-11,0.663835049
0.08333,45.0000013,224.999996,7.59097917e-13,0.663835585
0.08333,45.0000013,240.000007,6.99973326e-12,0.663835049
0.08333,45.0000013,255.000004,3.89681343e-11,0.663833797
0.08333,45.0000013,270.000001,9.42311576e-11,0.663833082
0.08333,45.0000013,284.999998,1.56817601e-10,0.663833797
0.08333,45.0000013,299.999995,2.01015038e-10,0.663835049
0.08333,45.0000013,314.999992,2.1228902e-10,0.663835585
0.08333,45.0000013,329.999989,1.95689701e-10,0.663835049
0.08333,45.0000013,345.000013,1.62577174e-10,0.663833678
0.08333,45.0000013,360.00001,1.19610113e-10,0.663833082
0.08333,60.0000017,0,2.64464534e-10,0.999831378
0.08333,60.0000017,15.0000004,1.54434562e-10,0.999833047
0.08333,60.0000017,30.0000008,5.38681218e-11,0.999836028
0.08333,60.0000017,45.0000013,1.71404438e-12,0.999837577
0.08333,60.0000017,60.0000017,2.32321419e-11,0.999836028
0.08333,60.0000017,74.9999987,1.03637522e-10,0.999833047
0.08333,60.0000017,90.0000025,2.08304943e-10,0.999831676
0.08333,60.0000017,105,3.1357697e-10,0.999833047
0.08333,60.0000017,120.000003,4.06610884e-10,0.999836028
0.08333,60.0000017,135,4.68799e-10,0.999837577
0.08333,60.0000017,149.999997,4.70491313e-10,0.999836028
0.08333,60.0000017,164.999994,3.9417325e-10,0.999833047
0.08333,60.0000017,180.000005,2.64387595e-10,0.999831378
0.08333,60.0000017,195.000002,1.34046177e-10,0.999833047
0.08333,60.0000017,209.999999,4.21460956e-11,0.999836028
0.08333,60.0000017,224.999996,1.69582761e-12,0.999837577
0.08333,60.0000017,240.000007,1.5866277e-11,0.999836028
0.08333,60.0000017,255.000004,8.72237838e-11,0.999833047
0.08333,60.0000017,270.000001,2.08351794e-10,0.999831676
0.08333,60.0000017,284.999998,3.44218515e-10,0.999833047
0.08333,60.0000017,299.999995,4.41347736e-10,0.999836028
0.08333,60.0000017,314.999992,4.68693473e-10,0.999837577
0.08333,60.0000017,329.999989,4.3446402e-10,0.999836028
0.08333,60.0000017,345.000013,3.6132225e-10,0.999833047
0.08333,60.0000017,360.00001,2.64464534e-10,0.999831378
0.08333,74.9999987,0,4.04069306e-10,1.24752045
0.08333,74.9999987,15.0000004,2.29066002e-10,1.24752307
0.08333,74.9999987,30.0000008,7.80540424e-11,1.24752772
0.08333,74.9999987,45.0000013,2.62711142e-12,1.2475301
0.08333,74.9999987,60.0000017,3.28389468e-11,1.24752796
0.08333,74.9999987,74.9999987,1.52820298e-10,1.24752307
0.08333,74.9999987,90.0000025,3.18272853e-10,1.24752045
0.08333,74.9999987,105,4.88081409e-10,1.24752307
0.08333,74.9999987,120.000003,6.3120531e-10,1.24752796
0.08333,74.9999987,135,7.15345061e-10,1.2475301
0.08333,74.9999987,149.999997,7.06045777e-10,1.24752772
0.08333,74.9999987,164.999994,5.90874849e-10,1.24752307
0.08333,74.9999987,180.000005,4.03963918e-10,1.24752045
0.08333,74.9999987,195.000002,2.1085797e-10,1.24752307
0.08333,74.9999987,209.999999,6.75901626e-11,1.24752772
0.08333,74.9999987,224.999996,2.61011547e-12,1.2475301
0.08333,74.9999987,240.000007,2.62591095e-11,1.24752796
0.08333,74.9999987,255.000004,1.3817425e-10,1.24752307
0.08333,74.9999987,270.000001,3.18337051e-10,1.24752045
0.08333,74.9999987,284.999998,5.15459897e-10,1.24752307
0.08333,74.9999987,299.999995,6.62257138e-10,1.24752796
0.08333,74.9999987,314.999992,7.15343729e-10,1.2475301
0.08333,74.9999987,329.999989,6.74007739e-10,1.24752772
0.08333,74.9999987,345.000013,5.61640512e-10,1.24752307
0.08333,74.9999987,360.00001,4.04069306e-10,1.24752045
0.08333,90.0000025,0,4.61999022e-10,1.33854401
0.08333,90.0000025,15.0000004,2.51170362e-10,1.33854699
0.08333,90.0000025,30.0000008,8.27910379e-11,1.33855271
0.08333,90.0000025,45.0000013,3.00353275e-12,1.33855546
0.08333,90.0000025,60.0000017,3.37403577e-11,1.33855271
0.08333,90.0000025,74.9999987,1.66223049e-10,1.33854699
0.08333,90.0000025,90.0000025,3.639051e-10,1.33854425
0.08333,90.0000025,105,5.73373904e-10,1.33854699
0.08333,90.0000025,120.000003,7.39050543e-10,1.33855271
0.08333,90.0000025,135,8.17466539e-10,1.33855546
0.08333,90.0000025,149.999997,7.88037857e-10,1.33855271
0.08333,90.0000025,164.999994,6.58218591e-10,1.33854699
0.08333,90.0000025,180.000005,4.61882532e-10,1.33854401
0.08333,90.0000025,195.000002,2.51093729e-10,1.33854699
0.08333,90.0000025,209.999999,8.27514446e-11,1.33855271
0.08333,90.0000025,224.999996,2.99441093e-12,1.33855546
0.08333,90.0000025,240.000007,3.37565774e-11,1.33855271
0.08333,90.0000025,255.000004,1.66264363e-10,1.33854699
0.08333,90.0000025,270.000001,3.63976016e-10,1.33854425
0.08333,90.0000025,284.999998,5.73479764e-10,1.33854699
0.08333,90.0000025,299.999995,7.3919082e-10,1.33855271
0.08333,90.0000025,314.999992,8.17630574e-10,1.33855546
0.08333,90.0000025,329.999989,7.88206e-10,1.33855271
0.08333,90.0000025,345.000013,6.58368415e-10,1.33854699
0.08333,90.0000025,360.00001,4.61999022e-10,1.33854401
0.08333,105,0,4.04069306e-10,1.24752057
0.08333,105,15.0000004,2.10708131e-10,1.24752307
0.08333,105,30.0000008,6.72303047e-11,1.24752772
0.08333,105,45.0000013,2.61616965e-12,1.2475301
0.08333,105,60.0000017,2.66377094e-11,1.24752796
0.08333,105,74.9999987,1.38355521e-10,1.24752307
0.08333,105,90.0000025,3.1827288e-10,1.24752045
0.08333,105,105,5.15625764e-10,1.24752307
0.08333,105,120.000003,6.62567279e-10,1.24752796
0.08333,105,135,7.15196014e-10,1.2475301
0.08333,105,149.999997,6.73421985e-10,1.24752772
0.08333,105,164.999994,5.61246716e-10,1.24752307
0.08333,105,180.000005,4.03963918e-10,1.24752057
0.08333,105,195.000002,2.28775943e-10,1.24752307
0.08333,105,209.999999,7.76212219e-11,1.24752772
0.08333,105,224.999996,2.61669375e-12,1.2475301
0.08333,105,240.000007,3.32482444e-11,1.24752796
0.08333,105,255.000004,1.530778e-10,1.24752307
0.08333,105,270.000001,3.18337051e-10,1.24752045
0.08333,105,284.999998,4.88436347e-10,1.24752307
0.08333,105,299.999995,6.31764474e-10,1.24752796
0.08333,105,314.999992,7.15488113e-10,1.2475301
0.08333,105,329.999989,7.0575884e-10,1.24752772
0.08333,105,345.000013,5.90749838e-10,1.24752307
0.08333,105,360.00001,4.04069306e-10,1.24752057
0.08333,120.000003,0,2.64464478e-10,0.999831378
0.08333,120.000003,15.0000004,1.33883321e-10,0.999832869
0.08333,120.000003,30.0000008,4.17817655e-11,0.999835908
0.08333,120.000003,45.0000013,1.69906689e-12,0.999837399
0.08333,120.000003,60.0000017,1.6242372e-11,0.999835908
0.08333,120.000003,74.9999987,8.74086845e-11,0.999832869
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... 19202 more lines ...

Draft

Mon Nov 8 17:04:30 2021

Ethan Fahimi

11/04/2021 AREA run 2 violin plot

This is a plot made from the AREA project with full Arasim implementation with each gain pattern of each individual being fixed across all frequencies.

This run was done with 50 total individuals per generation, across 36 generations. Each individual was tested with 4 seeds of 10,000 neutrinos, for a total of 40,000 neutrinos. For each new generation, 25 individuals were created with roulette crossover, 8 with roulette mutation, 9 with tournament crossover, and 8 with tournament mutation.

Attachment 1: 20211104fahimi5run2.png

138

Fri Sep 17 13:41:36 2021

Ethan Fahimi

07/20/2021 AREA run 3 violin plot

This is a plot made from the AREA project with full Arasim implementation. It can be seen that the Veff of any individuals is not what I would consider "good", nor is it really rising, it is quite flat. This is because in this version of AREA, the gain pattern at each frequency is generated differently than each other frequency, there is no correlation. This is known and actively being corrected. This plot is of old data and was just made for two reasons: to make sure that the violin plotting script works for AREA, to display this early form of AREA that has been adapted for full Arasim.

This plot is further detailed in Julie Rolla's doctorate thesis.

Attachment 1: Image_9-13-21_at_6.35_PM.jpg

140

Mon Nov 8 17:27:01 2021

Ethan Fahimi

07/20/2021 AREA run 3 violin plot

This is a plot made from the AREA project with full Arasim implementation with each gain pattern of each individual being fixed across all frequencies.

individual 32 in gen 20 and individual 35 in gen 27 look promising (they have Veff > 8)

Attachment 1: 20211104fahimi5run2.png

216

Tue May 9 18:09:35 2023

Alex M

05/08/23 Pueo Run

Here are the run details for the latest PUEO run we've started. There are still some bugs that need to be worked out, which are detailed on the github. Here is the directory where the data is stored: /fs/ess/PAS1960/HornEvolutionOSC/GENETIS_PUEO/BiconeEvolution/current_antenna_evo_build/XF_Loop/Evolutionary_Loop/Run_Outputs/2023_05_08

This run uses 50 individuals per generation with 400k neutrinos per individual at an energy exponent of 19. Only the inner side length and outer sidelength are being evolved (which evolves the height since the opening angle is fixed).

Issues With Part E (Dylan):

The Plots were not automatically created for the first generation. After a quick look through, I found that the fitness score and v effective csv files were being moved before they were copied, so the files didn’t end up in the correct place. Additionally, the errorbars.csv file was not being created, so I made a temporary fix to create a file of 0 error bars to allow for plotting the values while I work on getting the real error values.

Update: I have modified Will’s script for reading the root file outputs, so it can now read them to output a CSV file with the effective volume along with its positive and negative errors. This script does the same and more as the fitnessfunctionPUEO.py, so I will replace it in the loop when there is downtime. Additionally, this script means we don’t need to output a veff.csv file from pueoSim. I will now work on creating a less “janky” version of my pueoSim change for reading in the gain files, so I can get Will to officially add it to pueoSim and we can pull any updates in the future.

Update, Implementing the new script into Part E:

The rootAnalysis.py script is very picky with environment variables. So, first I had to load and then unload a version of python to make sure the default version is loaded. Then, I moved the sourcing of set_plotting_env.sh to later in the script to avoid having an alternate version of root sourced while running (this would cause errors). Then I source the environment for pueosim (path hardcoded, change when loop isn’t running) and loop through the rootAnalysis.py program for each individual in the generation. This will output a ${gen}_fitnessScores.csv and a ${gen}_errorBars.csv in the run directory for plotting script to use. Because it outputs these automatically, I commented out the old methods we used to create these files and removed the temporary error bar fix as well.

Another Update:

We paused the loop. I changed the hardcoded parts, and we pushed the new updates to the github. I will make comments on the changes later today.

Wednesday:

It seems like the loop is still not creating the csv files or plots for generation 1 or 2. Alex gave me the error message. The python script rootAnalysis.py had an issue with the include Geoid.h line. This was caused by sourcing the wrong things while trying to get the script working. I found that I only changed my local pueoSim environment to include the fftw installation to the $PATH and $LD_LIBRARY_PATH variables. So, I changed /fs/ess/PAS1960/buildingPueoSim/set_env.sh as well. Also, I found that the include statements in rootAnalysis.py were missing the PAS1960 portion of the path. After fixing these, and adding a missing ‘/’ to the output file path, I manually ran the rootAnalysis.py program for the 2023_05_08 run, mimicking the portion of the bash script that runs it in Part_E. It outputted the correct files in the correct format. I then ran the FScorePlot script. The median line for the ViolinPlot seemed wrong, and the FScorePlot was too scrunched with a y start of 0; I will need to change these.

Plotting Update (Dylan):

Ok, plots still aren’t being made, and I’m not running the loop, so I don’t have access to the error messages, so I’ll go through everything one by one. For Veff_Plots, this isn’t being made as there are currently no vEffectives.csv. This isn’t a big deal, as it’s just a copy of FScorePlot, but I added the creation of vEffectives.csv to rootAnalysis.py anyway. Next, I noticed that runData.csv, which is required for a couple of the plots was not being made. I looked, and the version of gensData.py had the old values for the skiprows when reading in the fitnessScores and generationDNA files, something that was overlooked when we merged the version I was developing with the version Alex was developing on. I can’t access the directory or the file, I think this is why it was overlooked in the merge. I created a temporary PUEO version in Antenna_Performance_Metric (I’m also fine with it just living here permanently).

Also, the csv files are now in the GenerationData/ directory in the run directory? This affects every plotting script and they will not work without changes. I don’t know why this was changed or if this change is permanent?

Next, ok apparently, VariablePlots isn’t even a file in the loop? We really need to use GitHub better.

I moved my local version of the program into the loop and it ran fine manually.

I am forsaking the Generation_Data directory, so I changed the rainbowPlotter and dataConverter scripts to read in a location to match all the other plotting scripts. They both also ran fine manually.

Note: The rainbowPlotter script should be able to create a gradient from the minimum fitness score to the maximum fitness score. (currently, the range is hardcoded and this can cause basically a mono-color graph.)

FScorePlot should be good

The bash script was inputting 5 variables into colorplots when the pueo version only takes in 4 (this is also something that was already fixed before the merge.) It also requires the vEffective.csv files. After copying over the fitnessScore.csv files to vEffective.csv files, it ran fine. (The vEffective.csv files will be made automatically by rootAnalysis.py in the future)

Attachment 1: run_details.txt

####### VARIABLES: LINES TO CHECK OVER WHEN STARTING A NEW RUN ###############################################################################################
RunName='2023_05_08'	## This is the name of the run. You need to make a unique name each time you run.
TotalGens=10			## number of generations (after initial) to run through
NPOP=50			## number of individuals per generation; please keep this value below 99
Seeds=10			## This is how many AraSim jobs will run for each individual## the number frequencies being iterated over in XF (Currectly only affects the output.xmacro loop)
FREQ=60				## the number frequencies being iterated over in XF (Currectly only affects the output.xmacro loop)
NNT=40000			## Number of Neutrinos Thrown in AraSim   
exp=19				## exponent of the energy for the neutrinos in AraSim
ScaleFactor=1.0			## ScaleFactor used when punishing fitness scores of antennae larger than the drilling holes
GeoFactor=1			## This is the number by which we are scaling DOWN our antennas. This is passed to many files
num_keys=6			## how many XF keys we are letting this run use
database_flag=0			## 0 if not using the database, 1 if using the database
				## These next 3 define the symmetry of the cones.
PUEO=1				## IF 1, we evolve the PUEO quad-ridged horn antenna, if 0, we evolve the Bicone
RADIUS=1			## If 1, radius is asymmetric. If 0, radius is symmetric		
LENGTH=1			## If 1, length is asymmetric. If 0, length is symmetric
ANGLE=1				## If 1, angle is asymmetric. If 0, angle is symmetric
CURVED=1			## If 1, evolve curved sides. If 0, sides are straight
A=1				## If 1, A is asymmetric
B=1				## If 1, B is asymmetric
SEPARATION=0    		## If 1, separation evolves. If 0, separation is constant
NSECTIONS=2 			## The number of chromosomes
DEBUG_MODE=0			## 1 for testing (ex: send specific seeds), 0 for real runs
				## These next variables are the values passed to the GA
REPRODUCTION=3			## Number (not fraction!) of individuals formed through reproduction
CROSSOVER=36			## Number (not fraction!) of individuals formed through crossover
MUTATION=1			## Probability of mutation (divided by 100)
SIGMA=5				## Standard deviation for the mutation operation (divided by 100)
ROULETTE=20			## Percent of individuals selected through roulette (divided by 10)
TOURNAMENT=20			## Percent of individuals selected through tournament (divided by 10)
RANK=60				## Percent of individuals selected through rank (divided by 10)
ELITE=0				## Elite function on/off (1/0)

Draft

Wed May 20 10:58:38 2020

Today's Summer 2020 daily update:

As a note, today OSC was down so productivity was more limited

Name	Update for Today	Plans for Tomorrow
Alex M.	Mostly just wrote more on the paper in the Genetic Algorithm section. I added some citation that we used in ICRC but there are still more places that should have citations.	I might check tonight when OSC is back up to try to push in more updates to the loop because I wanna get Evelyn and Ryan started on running the loop. Putting in those fixes is a big priority because we want to be able to correct the potential issue with XF simulation folders being overwritten and thus uan data not corresponding to the write individuals. The two big things for me in the loop are getting the simulation data to save correctly (and also putting that in the database) and testing that we can replicate results using the specific seed. I'll probably only focus on loop stuff tomorrow.
Alex P.	Got up before OSC was down to check progress of overnight run, it seems to have worked but I noticed a problem with the database that it wasn't writing to it probably due to a permissions issue but I would have to run another time to see. Shouldn't have affected data but just the use of the database. Run got up to 8 generations with non-zero fitness score which is positive and seems to have fixed the error we originally encountered. Talked to Eliot about pointers and possible errors but was unable to look at the specific error because it is on OSC.	Tomorrow plan is to continue to work on database functionality and continue run to get more generations, also want to add the ability to add more plots than just the fitness score to the dropbox automatically. Plots: upload all plots (Fitness, LRT, vEff), remove legend, upload penalized red/green plot too, take off legend, add units to Fitness
Leo
Eliot	Read about pointers and vectors in C++. Talked to Alex P a bit, and have some ideas of things to change to get the GA running. Began reading about antennas. Mostly a down day due to OSC being down.	Will implement changes to GA and continue familiarizing myself with how XF reads these values.
Evelyn
Ryan

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